de.jstacs.parameters

Class SequenceScoringParameterSet<T extends InstantiableFromParameterSet>

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.parameters.SequenceScoringParameterSet<T>

Type Parameters:

T - the type of the SequenceScoringParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

BayesianNetworkDiffSMParameterSet, DGTrainSMParameterSet, SamplingScoreBasedClassifierParameterSet, ScoreClassifierParameterSet

public abstract class SequenceScoringParameterSet<T extends InstantiableFromParameterSet>
extends InstanceParameterSet<T>

Abstract class for a ParameterSet containing all parameters necessary to construct an Object that implements InstantiableFromParameterSet. This parameter set handles the AlphabetContainer and if necessary the length of a sequence, so it is well suited as parameter set for AbstractTrainableStatisticalModel and AbstractClassifier.

Author:

Jan Grau, Jens Keilwagen

See Also:

InstantiableFromParameterSet, ParameterSet, AbstractTrainableStatisticalModel, AbstractClassifier

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields

Modifier and Type	Field and Description
protected Parameter	alphabet The alphabet the model works on
protected Parameter	length The length of sequences the model can work on or 0 for arbitrary length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Constructor and Description
SequenceScoringParameterSet(Class<T> instanceClass, AlphabetContainer.AlphabetContainerType type, boolean simple) Constructs an InstanceParameterSet having empty parameter values.
SequenceScoringParameterSet(Class<T> instanceClass, AlphabetContainer.AlphabetContainerType type, boolean simple, boolean variableLength) Constructs a SequenceScoringParameterSet having empty parameter values.
SequenceScoringParameterSet(Class<T> instanceClass, AlphabetContainer alphabet) Constructs a SequenceScoringParameterSet for an object that can handle sequences of variable length and with the AlphabetContainer alphabet.
SequenceScoringParameterSet(Class<T> instanceClass, AlphabetContainer alphabet, int length, boolean variableLength) Constructs a SequenceScoringParameterSet from an AlphabetContainer and the length of a sequence.
SequenceScoringParameterSet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
SequenceScoringParameterSet<T>	clone() Creates a full clone (deep copy) of this ParameterSet.
boolean	equals(Object o)
protected void	fromXML(StringBuffer representation) Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().
AlphabetContainer	getAlphabetContainer() Returns the AlphabetContainer of the current instance.
int	getLength() Returns the length of the sequences the model can work on.
int	getNumberOfParameters() Returns the number of parameters in the ParameterSet.
Parameter	getParameterAt(int i) Returns the Parameter at position i.
boolean	hasDefaultOrIsSet() Returns true if all parameters in this ParameterSet are either set by the user or have default values.
void	reset() Resets all Parameters in this ParameterSet to their default values or null if not default value was provided.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass, getInstanceComment, getInstanceName

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

alphabet

protected Parameter alphabet

The alphabet the model works on

length

protected Parameter length

The length of sequences the model can work on or 0 for arbitrary length

Constructor Detail

SequenceScoringParameterSet

public SequenceScoringParameterSet(Class<T> instanceClass,
                                   AlphabetContainer.AlphabetContainerType type,
                                   boolean simple)

Constructs an InstanceParameterSet having empty parameter values. This constructor should only be used if the object can handle sequences of fixed length.

Parameters:

instanceClass - the class of the instance

type - the type of the alphabet(s)

simple - determines whether the alphabet should be simple

See Also:

AlphabetContainer.AlphabetContainerType

SequenceScoringParameterSet

public SequenceScoringParameterSet(Class<T> instanceClass,
                                   AlphabetContainer.AlphabetContainerType type,
                                   boolean simple,
                                   boolean variableLength)

Constructs a SequenceScoringParameterSet having empty parameter values. The user can specify a-priori if the object can handle sequences of variable lengths. If that is the case the object is not queried from the user as it is 0 anyway.

Parameters:

instanceClass - the (sub-)class of the instance

type - the type of the alphabet(s)

simple - determines whether the alphabet should be simple

variableLength - true if the object can handle sequences of arbitrary length, false otherwise

See Also:

AlphabetContainer.AlphabetContainerType

SequenceScoringParameterSet

public SequenceScoringParameterSet(StringBuffer representation)
                            throws NonParsableException

The standard constructor for the interface Storable. Constructs a SequenceScoringParameterSet from its XML representation. Automatically calls the current implementation of fromXML(StringBuffer).

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer representation could not be parsed

SequenceScoringParameterSet

public SequenceScoringParameterSet(Class<T> instanceClass,
                                   AlphabetContainer alphabet,
                                   int length,
                                   boolean variableLength)
                            throws Exception

Constructs a SequenceScoringParameterSet from an AlphabetContainer and the length of a sequence. This constructor can be used to implement a SequenceScoringParameterSet that is already instantiated with known parameter values.

Parameters:

instanceClass - the class of the instance

alphabet - the AlphabetContainer for a sequence

length - the length of sequence

variableLength - true if the object can handle sequences of arbitrary length, false otherwise

Throws:

Exception - if the alphabets or the length are not in the expected range of values

SequenceScoringParameterSet

public SequenceScoringParameterSet(Class<T> instanceClass,
                                   AlphabetContainer alphabet)
                            throws Exception

Constructs a SequenceScoringParameterSet for an object that can handle sequences of variable length and with the AlphabetContainer alphabet. This constructor can be used to implement a SequenceScoringParameterSet that is already instantiated with known parameter values.
The length parameter is set to 0.

Parameters:

instanceClass - the (sub-)class of the instance

alphabet - the AlphabetContainer for a sequence

Throws:

Exception - if the alphabets or the length are not in the expected range of values

Method Detail

hasDefaultOrIsSet

public boolean hasDefaultOrIsSet()

Description copied from class: ParameterSet

Returns true if all parameters in this ParameterSet are either set by the user or have default values. If any additional constraints are required on your parameters you should either specify some ParameterValidator on these parameters or implement these constraints by overriding this method in your implementation of ParameterSet. It is recommended to specify a useful remark which constraint failed in the member-variable errorMessage, which will be displayed to the user. In the overriding method super.ParameterSet.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:

hasDefaultOrIsSet in class ParameterSet

Returns:

true if all parameters have some allowed value set, false otherwise

reset

public void reset()

Description copied from class: ParameterSet

Resets all Parameters in this ParameterSet to their default values or null if not default value was provided.

Overrides:

reset in class ParameterSet

See Also:

Parameter.reset()

getAlphabetContainer

public AlphabetContainer getAlphabetContainer()

Returns the AlphabetContainer of the current instance.

Returns:

the AlphabetContainer

getLength

public int getLength()
              throws IllegalArgumentException

Returns the length of the sequences the model can work on.

Returns:

the length of the sequences the model can work on

Throws:

IllegalArgumentException - if the length is not correct, i.e. the length is not suitable for the chosen requirements

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: ParameterSet

Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().

Overrides:

fromXML in class InstanceParameterSet<T extends InstantiableFromParameterSet>

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

ParameterSet.toXML()

getNumberOfParameters

public int getNumberOfParameters()

Description copied from class: ParameterSet

Returns the number of parameters in the ParameterSet.

Overrides:

getNumberOfParameters in class ParameterSet

Returns:

the number of parameters in the ParameterSet

getParameterAt

public Parameter getParameterAt(int i)

Description copied from class: ParameterSet

Returns the Parameter at position i.

Overrides:

getParameterAt in class ParameterSet

Parameters:

i - the position in the ParameterSet

Returns:

the Parameter at position i

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class InstanceParameterSet<T extends InstantiableFromParameterSet>

Returns:

the XML representation

equals

public boolean equals(Object o)

Overrides:

equals in class Object

clone

public SequenceScoringParameterSet<T> clone()
                                     throws CloneNotSupportedException

Description copied from class: ParameterSet

Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:

• Create a new instance of your subclass of ParameterSet, most likely with an empty constructor or the one taking just the instance class.
• Call this.fillWithStandardFieldsForClone on this instance.
• Return the instance.

This method fulfills the conventions of Object's method Object.clone().

Overrides:

clone in class ParameterSet

Returns:

a deep clone/copy of this ParameterSet

Throws:

CloneNotSupportedException